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BMRB: 18132

4AAI

THERMOSTABLE PROTEIN FROM HYPERTHERMOPHILIC VIRUS SSV-RH

Authors

Schlenker, C., Goel, A., Tripet, B.P., Menon, S., Lawrence, C.M., Copie, V.

Assembly

THERMOSTABLE PROTEIN FROM HYPERTHERMOPHILIC VIRUS SSV-RH

Entity

1. THERMOSTABLE PROTEIN FROM HYPERTHERMOPHILIC VIRUS SSV-RH (polymer, Thiol state: not present), 73 monomers, 8624.088 × 2 Da Detail

MVESKKIAKK KTTLAFDEDV YHTLKLVSVY LNRDMTEIIE EAVVMWLIQN KEKLPNELKP KIDEISKRFF PAK

Total weight

17248.176 Da

Max. entity weight

8624.088 Da

Source organism

Sulfolobus virus Ragged Hills

Exptl. method

Refine. method

ENERGY MINIMIZATION

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 60.3 %, Completeness (bb): 74.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	60.3 % (561 of 930)	61.0 % (299 of 490)	52.9 % (193 of 365)	92.0 % (69 of 75)
Backbone	74.1 % (320 of 432)	84.6 % (121 of 143)	59.4 % (130 of 219)	98.6 % (69 of 70)
Sidechain	51.0 % (291 of 571)	51.3 % (178 of 347)	51.6 % (113 of 219)	0.0 % (0 of 5)
Aromatic	0.0 % (0 of 62)	0.0 % (0 of 31)	0.0 % (0 of 30)	0.0 % (0 of 1)
Methyl	62.0 % (57 of 92)	71.7 % (33 of 46)	52.2 % (24 of 46)

1. ORF E73

MVESKKIAKK KTTLAFDEDV YHTLKLVSVY LNRDMTEIIE EAVVMWLIQN KEKLPNELKP KIDEISKRFF PAK

Show sample condition

Sample

Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 4AAI, Strand ID: A, B Detail

Release date

2012-03-22

Citation

Structural studies of E73 from a hyperthermophilic archaeal virus identify the "RH3" domain, an elaborated ribbon-helix-helix motif involved in DNA recognition
Schlenker, C., Goel, A., Tripet, B.P., Menon, S., Willi, T., Dlakic, M., Young, M.J., Lawrence, C., Copie, V.
Biochemistry (2012), 51, 2899-2910, PubMed 22409376 , DOI 10.1021/bi201791s , Abstract

Related entities 1. THERMOSTABLE PROTEIN FROM HYPERTHERMOPHILIC VIRUS SSV-RH, : 1 : 1 entities Detail

Experiments performed 9 experiments Detail

1 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

2 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

3 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

4 3D H(CCO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

5 3D HNCA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

6 2D 1H-13C HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

7 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

8 3D HCCH-TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

9 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system PMSF 1 MM, SODIUM AZIDE 0. 01 %, POTASSIUM PHOSPHATE 50 MM, D2O 10 %, EDTA 1 MM, Pressure 1.000 atm, Temperature 312.000 K, pH 5.000, Details 1 mM

#	Name	Isotope labeling	Type	Concentration
1	PMSF	[U-13C; U-15N]		1 mM
2	SODIUM AZIDE	natural abundance		0.01 %
3	POTASSIUM PHOSPHATE	natural abundance		50 mM
4	EDTA	natural abundance		1 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18132_4aai.nef
Input source #2: Coordindates	4aai.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70---
MVESKKIAKKKTTLAFDEDVYHTLKLVSVYLNRDMTEIIEEAVVMWLIQNKEKLPNELKPKIDEISKRFFPAK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVESKKIAKKKTTLAFDEDVYHTLKLVSVYLNRDMTEIIEEAVVMWLIQNKEKLPNELKPKIDEISKRFFPAK

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50--------60--------70---
MVESKKIAKKKTTLAFDEDVYHTLKLVSVYLNRDMTEIIEEAVVMWLIQNKEKLPNELKPKIDEISKRFFPAK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVESKKIAKKKTTLAFDEDVYHTLKLVSVYLNRDMTEIIEEAVVMWLIQNKEKLPNELKPKIDEISKRFFPAK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	0	0	100.0
B	B	73	0	0	100.0

Content subtype: combined_18132_4aai.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	509		100.0 (chain: A, length: 73)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3890 (1)	noe	100.0 (chain: A, length: 73), 100.0 (chain: B, length: 73)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	100 (1)	hbond	52.1 (chain: A, length: 73), 52.1 (chain: B, length: 73)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	244 (244)	.	90.4 (chain: A, length: 73), 90.4 (chain: B, length: 73)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 269
  - ¹³C chemical shifts: 171
  - ¹⁵N chemical shifts: 69
- Completeness of assignments
  - Entity_assemble_ID: A
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 73, Sequence coverage: 100.0%
- Total number of restraints: 3838
- Weight of restraints: 1.0 (3838)
- Potential type of restraints: square-well-parabolic (3838)
- Range of distance target values: 2.4, 4.15 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 52.1%
    - Entity_assembly_ID: B, Chain length: 73, Sequence coverage: 52.1%
  - Total number of restraints: 100
  - Weight of restraints: 1.0 (100)
  - Potential type of restraints: square-well-parabolic (100)
  - Range of distance target values: 1.9, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 90.4%
  - Entity_assembly_ID: B, Chain length: 73, Sequence coverage: 90.4%
- Total number of restraints: 244
- Total number of restraints per polymer type: 244
- Weight of restraints: 1.0 (244)
- Potential type of restraints: square-well-parabolic (244)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords ARCHAEA, DNA-BINDING PROTEINS, EXTREMOPHILE, RIBBON-HELIX-HELIX PRO DNA-BINDING PROTEINS, RIBBON-HELIX-HELIX PROTEINS, VIRAL PROTEIN